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1,000 results • Page
4 of 20
Sort: Views
Rank
Views
Votes
Replies
60
votes
3
replies
32k
views
Paired-end reads - what is what?
RNA-Seq
updated 5 months ago by
Ram
39k • written 8.0 years ago by
darxsys
▴ 220
60
votes
17
replies
31k
views
16 follow
Scientific Names In Blast Output And Databases
blast
blast+
updated 5 months ago by
Ram
39k • written 9.9 years ago by
Carlos Borroto
★ 2.0k
94
votes
25
replies
31k
views
11 follow
Tutorial:
Fastq Quality Control Shootout
quality
qc
trimming
fastq
updated 3 months ago by
Ram
39k • written 10.7 years ago by
Istvan Albert
98k
27
votes
11
replies
31k
views
8 follow
Samtools View: Only Forward Or Reverse Strand
samtools
strand
updated 11 months ago by
Ram
39k • written 11.6 years ago by
Gregor Rot
▴ 540
37
votes
11
replies
31k
views
8 follow
Wright'S Fst And Weir & Cockerham'S Fst Estimator - Simple Explanation Of The Difference
fst
population-genetics
updated 5 months ago by
Ram
39k • written 9.9 years ago by
confusedious
▴ 450
197
votes
27
replies
31k
views
20 follow
Bioinformatics Cartoon
bioinformatics
updated 3 months ago by
Ram
39k • written 11.4 years ago by
Maxime Lamontagne
★ 2.3k
251
votes
36
replies
31k
views
27 follow
Forum:
How Do You Manage Your Files & Directories For Your Projects ?
project-management
file-management
updated 10 weeks ago by
Ram
39k • written 13.1 years ago by
Pierre Lindenbaum
154k
60
votes
17
replies
31k
views
7 follow
how to remove multiallelic from VCF
SNP
updated 4 months ago by
Ram
39k • written 8.1 years ago by
xinhui.wang
▴ 510
89
votes
19
replies
31k
views
12 follow
Tutorial:
Machine Learning For Cancer Classification - Part 1 - Preparing The Data Sets
microarray
bioconductor
expression
classification
updated 3 months ago by
Ram
39k • written 9.6 years ago by
Obi Griffith
20k
20
votes
9
replies
31k
views
8 follow
Biomart Bioconductor - Retrieving All Entrezgenes Of Hsapiens_Gene_Ensembl
biomart
r
bioconductor
updated 4 weeks ago by
Kevin Blighe
85k • written 10.9 years ago by
sthait
▴ 120
2
votes
6
replies
30k
views
how to install samtools
next-gen-sequencing
updated 10 months ago by
Ram
39k • written 7.4 years ago by
Chenglin
▴ 250
99
votes
16
replies
30k
views
18 follow
Tutorial:
Heatmaps in R
heatmap
R
updated 12 weeks ago by
Ram
39k • written 6.8 years ago by
Jean-Karim Heriche
26k
34
votes
12
replies
30k
views
8 follow
Forward Strand Or Reverse Strand
read
strand
updated 11 months ago by
Ram
39k • written 10.5 years ago by
siyu
▴ 150
27
votes
27
replies
30k
views
10 follow
Split Fastq Files Into Chunks Of 1M Reads
split
fastq
updated 10 months ago by
opplatek
▴ 240 • written 11.9 years ago by
Bioscientist
★ 1.7k
130
votes
123
replies
30k
views
23 follow
Tutorial:
Survival analysis with gene expression
cox
gene-expression
survival-analysis
geo
updated 11 weeks ago by
1769mkc
★ 1.1k • written 4.6 years ago by
Kevin Blighe
85k
43
votes
21
replies
30k
views
16 follow
Multi-Sample Vcf To Phylogenetic Tree.
vcf
updated 4 months ago by
Ram
39k • written 9.7 years ago by
William
★ 5.2k
9
votes
3
replies
30k
views
Bioconductor : Setting local install directory for packages
RNA-Seq
bioconductor
updated 10 months ago by
Ram
39k • written 7.7 years ago by
irritable_phd_syndrome
▴ 130
30
votes
12
replies
30k
views
6 follow
How To Interpret The Flag Field In The Sam Specification
bam
updated 8 months ago by
Ram
39k • written 10.7 years ago by
deepthithomaskannan
▴ 360
117
votes
59
replies
30k
views
23 follow
Help a graduate student going into Bioinformatics looking for a new personal laptop. Should I get a Mac or a PC?
hardware
next-gen
updated 4 months ago by
Ram
39k • written 8.1 years ago by
Angelo Victoria
▴ 30
7
votes
10
replies
30k
views
6 follow
Converting Sam To Bam
bam
sam
updated 5 months ago by
Ram
39k • written 11.4 years ago by
Haluk
▴ 190
10
votes
10
replies
30k
views
7 follow
How To Download .Gbk Files From Ncbi Website
ncbi
genbank
updated 10 weeks ago by
Ram
39k • written 11.5 years ago by
Arun
• 0
25
votes
35
replies
30k
views
16 follow
Calculate The Frequency Of Nucleotides At Each Position In An Mpileup File
mpileup
updated 4 months ago by
Jan Röslein
▴ 10 • written 9.2 years ago by
komal.rathi
★ 4.1k
8
votes
6
replies
30k
views
6 follow
Where To Download Hg19 Gene Annotation, Transcript Annotation And Cdna Fasta Files?
hg19
ucsc
updated 5 months ago by
Ram
39k • written 10.0 years ago by
Shaojiang Cai
▴ 100
12
votes
26
replies
29k
views
getting intersect between two lists of genes in R
gene
R
updated 10 months ago by
Ram
39k • written 7.6 years ago by
fi1d18
★ 4.2k
5
votes
6
replies
29k
views
Computing fold change values for RT-PCR
RT-PCR
Fold-change
updated 5 months ago by
Ram
39k • written 8.0 years ago by
Zara
▴ 20
6
votes
25
replies
29k
views
14 follow
CluserProfiler message "No gene can be mapped"
R
updated 7 days ago by
13554221497
• 0 • written 5.2 years ago by
ARich
▴ 130
16
votes
15
replies
29k
views
8 follow
C program to find complementary of DNA sequence
dna
c
updated 10 months ago by
Ram
39k • written 7.5 years ago by
Arindam Ghosh
▴ 500
152
votes
44
replies
29k
views
29 follow
Which Bioinformatic Friendly Pipeline Building Framework?
scripting
updated 11 months ago by
Ram
39k • written 9.4 years ago by
Carlos Borroto
★ 2.0k
27
votes
5
replies
29k
views
question about GSEA
GSEA
interpretation
updated 11 months ago by
Ram
39k • written 8.3 years ago by
kanwarjag
★ 1.2k
78
votes
42
replies
29k
views
25 follow
Tutorial:
Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm
rna-seq
bioconductor
updated 4 weeks ago by
Ram
39k • written 9.6 years ago by
Irsan
★ 7.7k
27
votes
14
replies
29k
views
samtools (conversion from .sam to .bam) and sorting of .bam file
alignment
genome
next-gen-sequencing
updated 5 months ago by
Ram
39k • written 8.0 years ago by
ravi.uhdnis
▴ 220
10
votes
7
replies
28k
views
How To Batch Download Journal Papers (Pdf)?
papers
updated 10 weeks ago by
Ram
39k • written 10.9 years ago by
Hranjeev
★ 1.5k
82
votes
28
replies
28k
views
19 follow
Tutorial:
How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor
GenVisR
Graphics
R
updated 3 months ago by
Ram
39k • written 7.2 years ago by
Obi Griffith
20k
9
votes
12
replies
28k
views
6 follow
How To Download Gene Sequences From Ncbi Gene
ncbi
fasta
gene
updated 10 weeks ago by
Ram
39k • written 11.5 years ago by
Pierre
▴ 20
126
votes
44
replies
28k
views
16 follow
Forum:
Trimming adapter sequences - is it necessary?
NGS
adapter
RNA-Seq
updated 3 months ago by
Ram
39k • written 6.7 years ago by
Lars
▴ 970
17
votes
14
replies
28k
views
13 follow
Merge Paired-End Reads
fastq
updated 8 weeks ago by
Ram
39k • written 11.6 years ago by
Nicolas Rosewick
10k
74
votes
14
replies
28k
views
12 follow
Forum:
Bioinformatics Consulting Thoughts
consulting
updated 11 months ago by
Ram
39k • written 13.0 years ago by
Will
4.5k
30
votes
10
replies
28k
views
Sjdboverhang Option In Star
updated 11 months ago by
Thind amarinder
▴ 310 • written 9.3 years ago by
Martombo
★ 3.0k
100
votes
38
replies
28k
views
34 follow
Forum:
List of cloud genomics companies
cloud-genomics
updated 4 weeks ago by
Jeremy Leipzig
21k • written 9.6 years ago by
14134125465346445
★ 3.6k
50
votes
14
replies
28k
views
8 follow
Where To Download Pam50 Gene Set?
cancer
annotation
classification
updated 3 months ago by
Ram
39k • written 9.9 years ago by
user
▴ 930
154
votes
17
replies
28k
views
13 follow
What Are The Big Questions That Bioinformatics And Computational Biology Will Be Answering In The Next Few Years?
updated 11 months ago by
Ram
39k • written 11.4 years ago by
Sean Davis
26k
41
votes
18
replies
28k
views
16 follow
extract only geneID and gene symbol from GTF file
gtf
python
genome
updated 3 months ago by
Ram
39k • written 8.1 years ago by
catherine
▴ 220
19
votes
8
replies
27k
views
7 follow
Merging/Concatenating Vcf Files
vcftools
snp
indel
written 10.8 years ago by
bioinfo
▴ 830
1
vote
1
reply
27k
views
Tutorial:
Docker denied: requested access to the resource is denied
docker
updated 10 months ago by
Vincent Laufer
★ 2.9k • written 10 months ago by
kodwings
▴ 10
19
votes
9
replies
27k
views
7 follow
Can anyone suggest a good tutorial to learn RNA-seq analysis?
analysis
RNA-Seq
ngs
updated 21 days ago by
Ram
39k • written 5.6 years ago by
Arindam Ghosh
▴ 500
15
votes
8
replies
27k
views
Input GSEA Pre-ranked list
gene
next-gen
RNA-Seq
genome
software
updated 6 months ago by
Ram
39k • written 7.9 years ago by
stevenlang123
▴ 200
20
votes
10
replies
27k
views
Converstion of BED with scores into bigWig
bed
bigWig
updated 6 months ago by
Ram
39k • written 7.9 years ago by
Leszek
4.2k
28
votes
8
replies
27k
views
6 follow
What Is Ad (Allelic Depth) In 1000Genomes Vcf?
read
allele
genome
updated 11 months ago by
Maryam
▴ 10 • written 12.4 years ago by
Chronos
▴ 610
23
votes
1
reply
27k
views
Difference between NCBI non-redundant and refseq database
refseq
nr
updated 9 months ago by
Ram
39k • written 7.6 years ago by
hdy
▴ 160
9
votes
5
replies
27k
views
7 follow
DESeq2 analysis for multiple conditions
RNA-Seq
DESeq2
updated 5 months ago by
Ram
39k • written 8.0 years ago by
eager_learner
▴ 60
1,000 results • Page
4 of 20
Recent Votes
Comment: RNASeq gene labeling and mRNA filter from bulkRNA data.
Comment: Saving results from yeastgenome.org blastp search
Comment: snps from empty well, Illumina Sequencing
Extract sequences from a fastq file by a list of IDs
Answer: Extract sequences from a fastq file by a list of IDs
Answer: Differences in GTF files hg19 and hg38
Answer: CHiP-Seq Questions
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Comment: RNASeq gene labeling and mRNA filter from bulkRNA data.
by
Yeeshouw
• 0
I see, I believe I was running an older version or have missed the option, I have updated to v2.10.5 and can see this option now. Thank you…
Comment: Saving results from yeastgenome.org blastp search
by
GenoMax
130k
Looks like yeastgenome site does not provide a way to export or save the results in any other format. You could do the search over at NCBI …
Answer: Differences in GTF files hg19 and hg38
by
GenoMax
130k
Not sure where you got your GTF for GRCh38 from but [**one from GENCODE**][1] has the level info you are looking for. chr1 HAVANA…
Comment: CHiP-Seq Questions
by
B.N.
• 0
Thank you for the suggestions Dr. Stark.
Comment: Diff Bind Questions
by
B.N.
• 0
Thank you so much for the insight Dr. Stark!
Comment: Is PanCan data microarray or rna-seq
by
GenoMax
130k
This particular example ("GeneChip") is an array. Early TCGA samples may have been done using arrays and later sequenced. Appears to be thi…
Comment: ChatGPT optimized for bioinformatics questions
by
Sasha
▴ 280
Hoping to add functionality around this. Stay tuned. Big problem for our space that needs to be resolved.
Comment: Is PanCan data microarray or rna-seq
by
solarchan7
• 0
Hi, so this [paper](https://www.nature.com/articles/s41598-019-45165-4) uses the TCGA dataset and in the supplementary information, it ment…
Comment: counts matrix should be numeric, currently it has mode: character when using a c
by
Darked89
4.4k
Since the input file is named `normalized.csv` and the values look like floats most likely the counts have been already normalized somehow.
Comment: Embryo transcriptome
by
Basti
★ 1.6k
https://www.ebi.ac.uk/ena/browser/view/PRJEB11202 https://www.ebi.ac.uk/ena/browser/view/PRJNA153427
Comment: ChatGPT optimized for bioinformatics questions
by
ATpoint
72k
How is it trained on PubMed/papers? One major drawback of ChatGPT is that it wildly makes up papers that do not even exist but with great c…
Answer: sgRNA design
by
ATpoint
72k
gRNAs are single-stranded and by this they have a strand-specificity (depends where the PAM is) and that gives them an orientation.
Answer: counts matrix should be numeric, currently it has mode: character when using a c
by
ATpoint
72k
You have commas as decimal delimiters which interpreted as text. Just replace by dot and make numeric: ```r d <- data.frame(A=c("1,2", "3,…
Comment: snps from empty well, Illumina Sequencing
by
GenoMax
130k
> I receive illumina sequencing files with 96 wells, our lab leaves one > well empty. When I process the files with a SNP calling pipeline …
Answer: counts matrix should be numeric, currently it has mode: character when using a c
by
Darked89
4.4k
You can try: counts_data <- read.csv2("normalized.csv", header = TRUE) But as far as I know DESeq2 requires raw counts as inpu…
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